Fighters from Islamic State West Africa Province (ISWAP) launched a pre-dawn attack in trucks and on motorcycles on Sunday on the base in Sabon Gari in Borno State's Damboa district, the military sources said.
They set fire to the base along with army vehicles, the sources said, on condition of anonymity as they are not authorised to speak on the incident.
"We lost six soldiers in the ISWAP terrorists attack on the base after an intense gun battle," one of the officers said.
The soldiers were forced to withdraw, the officer added.
Fighter jets deployed from the regional capital Maiduguri 100 kilometres (62 miles) away struck the attackers as they retreated, said the second military officer, who gave the same toll.
"Air strikes against the fleeing terrorists resulted in multiple militant fatalities, the destruction of operational vehicles and their weaponry," the officer said, without giving a toll of ISWAP casualties.
Since 2009, northern Nigeria has been plagued by various jihadist groups, including Boko Haram and a rival faction the Islamic State in West Africa (ISWAP), as well as armed criminal groups.
Conflict has killed more than 40,000 people and displaced around two million from their homes in the northeast.
In November, five Nigerian troops were killed and 10 more injured when ISWAP fighters raided a base in Kareto village near the border with Niger.
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